A Unified Approach for Representing Structurally-Complex Models in SBML Level 3

The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.

The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page (http://sbml.org/Community/Wiki/SBML_Level_3_Proposals) which deal with model structure, namely comp, arrays, spatial, geom, dyn and multi. For each one, I consider how the requirements which motivated the package can be handled using Simile's unified approach. Although Simile has a declarative model-representation language (in both Prolog and XML syntax), I use Simile diagrams and equation syntax throughout, since this is more compact and readable than large chunks of XML.

The conclusion is that Simile can indeed meet most of the requirements of these various packages, using a generic set of constructs - basically, the multiple-instance submodel, the concept of a relationship (association) between submodels, and array variables. This suggests the possibility of having a single SBML Level 3 extension package similar to the Simile data model, rather than a series of separate packages. Such an approach has a number of potential advantages and disadvantages compared with having the current set of discrete packages: these are discussed in this paper

Declarative modelling in the ecological and environmental sciences

Most simulation models in ecological and environmental research are implemented as computer programs in a conventional programming language. This brief paper argues for a radically different approach, based on the representation of the model structure, relationships and equations in a declarative format (e.g. XML). Simulation code can then be generated from this, but in addition the model can be displayed and processed in a wide range of useful ways, greatly increasing the efficiency and effectiveness of the modelling process

Extended system dynamics modelling of the impacts of food system drivers on food security, livelihoods and the environment

Food security research programmes, such as Global Environmental Change and Food Systems (GECAFS) and the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), need to consider extremely complex systems, with many agricultural, environmental, social and economic subsystems interacting with each other on a variety of scales and at a variety of levels on each. This poses considerable challenges in terms of representing the current state of knowledge, exploring how these systems might evolve in the future in response to external drivers and human input, and displaying the behaviour of the many variables involved in a way which is meaningful for stakeholders and policy advisers

Environmental modelling and Web 2.0 - using Connotea to share XML-represented information

Much academic information can be represented in a structured way and published on the web as XML documents. Such information can then be displayed in a wide variety of ways, using different XSLT stylesheets. 

This presentation presents MultiGuise, a Web application which allows any of several XML documents to be displayed using any of several stylesheets. Both the documents and the stylesheets are bookmarked in Connotea, from where MultiGuise retrieves them using a special tag. This approach means that anyone can add documents and stylesheets, simply by bookmarking them in Connotea.

The approach is illustrated primarily with environmental models represented in XML, but also with examples from SBML (Systems Biology Markup Language) and philosophical arguments marked up in XML

Harms and benefits associated with psychoactive drugs: findings of an international survey of active drug users.

There have been several recent efforts in the UK and the Netherlands to describe the harms of psychoactive substances based on ratings of either experts or drug users. This study aimed to assess the perceived benefits as well as harms of widely used recreational drugs, both licit and illicit, in an international sample of drug users. The survey was hosted at https://www.internationaldrugsurvey.org/ and was available in three languages. Residents reported their experience of 15 commonly used drugs or drug classes; regular users then rated their harms and benefits. In all, 5791 individuals from over 40 countries completed the survey, although the majority were from English speaking countries. Rankings of drugs differed across 10 categories of perceived benefits. Skunk and herbal cannabis were ranked consistently beneficial, whilst alcohol and tobacco fell below many classified drugs. There was no correlation at all between users' harm ranking of drugs and their classification in schedules of the USA or ABC system in the UK. Prescription analgesics, alcohol and tobacco were ranked within the top 10 most harmful drugs. These findings suggest that neither the UK nor US classification systems act to inform users of the harms of psychoactive substances. It is hoped the results might inform health professionals and educators of what are considered to be both the harms and benefits of psychoactive substances to young people

Modelling Decision-Making in Rural Communities at the Forest Margin

The FLORES simulation model aims to capture the interactions between rural communities living at the forest margin and the resources that they depend upon, in order to provide decision-makers with a tool that they can use to explore the consequences of alternative policy options. A key component of the model is simulating how decision-making agents within the system (individuals, households and the whole village) go about making their decisions. The model presented here is based on an anthropological description of the rules and relationships that people use, rather than on the assumption that people behave in an economically optimal fashion. The approach addresses both short-term decision-making (primarily the allocation of labour to various activities on a weekly basis), and long-term strategic land-use planning, taking into account the variety of tenure and inheritance patterns that operate in real communities. The decision-making sub-model has been implemented in the Rantau Pandan (Sumatra) version of FLORES, using the Simile modelling environment

FLORES: Helping People to Realize Sustainable Futures

People usually know how they want their situation to change to secure a better future, but they do not always know how to change their situation. Initiatives intended to secure a better future do not always work as intended, and may have unintended side effects. Computer models can help advocates explore consequences of proposed initiatives, so they can make informed selections of alternatives, secure in the knowledge that consequences have been thoroughly investigated. By encouraging people to explore scenarios, models empower people to be more innovative and less dependent on technocrats. New software solves technical limitations, but the real issue is not software, but rather the provision of a supportive framework within which people can express and experiment with ideas. FLORES, the Forest Land Oriented Resource Envisioning System, provides such a framework to stimulate interdisciplinary collaboration between researchers, practitioners and clients. A recent prototype demonstrated the feasibility of FLORES. However, FLORES is not about software; it is about providing the means to explore the consequences of alternative scenarios. Ultimately, FLORES is not a physical package, but a user group and the interactions they have amongst themselves, and with the people involved in policy-making. Fostering this emerging network through workshops and technical support will enhance FLORES by offering a better understanding of the concept, and by allowing more people, especially those from developing countries, to influence the development of FLORES and the issues that can be explored within it